A Machine Learning Approach for Predicting Essentiality of Metabolic Genes

In: Braman, J.C. (eds) Synthetic Biology. Methods in Molecular Biology, vol 2760 (2024)

Authors:

Lilli J Freischem & Diego A Oyarzún

Abstract:

The identification of essential genes is a key challenge in systems and synthetic biology, particularly for engineering metabolic pathways that convert feedstocks into valuable products. Assessment of gene essentiality at a genome scale requires large and costly growth assays of knockout strains. Here we describe a strategy to predict the essentiality of metabolic genes using binary classification algorithms. The approach combines elements from genome-scale metabolic models, directed graphs, and machine learning into a predictive model that can be trained on small knockout data. We demonstrate the efficacy of this approach using the most complete metabolic model of Escherichia coli and various machine learning algorithms for binary classification.

Predictable decadal forcing of the North Atlantic jet speed by sub-polar North Atlantic sea surface temperatures

Weather and Climate Dynamics Copernicus Publications 4:4 (2023) 853-874

Authors:

Kristian Strommen, Tim Woollings, Paolo Davini, Paolo Ruggieri, Isla R Simpson

Abstract:

It has been demonstrated that decadal variations in the North Atlantic Oscillation (NAO) can be predicted by current forecast models. While Atlantic Multidecadal Variability (AMV) in sea surface temperatures (SSTs) has been hypothesised as the source of this skill, the validity of this hypothesis and the pathways involved remain unclear. We show, using reanalysis and data from two forecast models, that the decadal predictability of the NAO can be entirely accounted for by the predictability of decadal variations in the speed of the North Atlantic eddy-driven jet, with no predictability of decadal variations in the jet latitude. The sub-polar North Atlantic (SPNA) is identified as the only obvious common source of an SST-based signal across the models and reanalysis, and the predictability of the jet speed is shown to be consistent with a forcing from the SPNA visible already within a single season. The pathway is argued to be tropospheric in nature, with the SPNA-associated heating extending up to the mid-troposphere, which alters the meridional temperature gradient around the climatological jet core. The relative roles of anthropogenic aerosol emissions and the Atlantic Meridional Overturning Circulation (AMOC) at generating predictable SPNA variability are also discussed. The analysis is extensively supported by the novel use of a set of seasonal hindcasts spanning the 20th century and forced with prescribed SSTs.

Using probabilistic machine learning to better model temporal patterns in parameterizations: a case study with the Lorenz 96 model

Geoscientific Model Development Copernicus Publications 16:15 (2023) 4501-4519

Authors:

Raghul Parthipan, Hannah M Christensen, J Scott Hosking, Damon J Wischik

On the relationship between reliability diagrams and the ‘signal-to-noise paradox’

Geophysical Research Letters American Geophysical Union 50:14 (2023) e2023GL103710

Authors:

Kristian Strommen, Molly MacRae, Hannah Christensen

Abstract:

The ‘signal-to-noise paradox’ for seasonal forecasts of the winter NAO is often described as an ‘underconfident’ forecast and measured using the ratio-of-predictable components metric (RPC). However, comparison of RPC with other measures of forecast confidence, such as spread-error ratios, can give conflicting impressions, challenging this informal description. We show, using a linear statistical model, that the ‘paradox’ is equivalent to a situation where the reliability diagram of any percentile forecast has a slope exceeding 1. The relationship with spread-error ratios is shown to be far less direct. We furthermore compute reliability diagrams of winter NAO forecasts using seasonal hindcasts from the European Centre for Medium-range Weather Forecasts and the UK Meteoro logical Office. While these broadly exhibit slopes exceeding 1, there is evidence of asymmetry between upper and lower terciles, indicating a potential violation of linearity/Gaussianity. The limitations and benefits of reliability diagrams as a diagnostic tool are discussed.

Robustness of the stochastic parameterization of sub-grid scale wind variability in sea-surface fluxes

Monthly Weather Review American Meteorological Society 151:10 (2023) 2587-2607

Authors:

Kota Endo, Adam H Monahan, Julie Bessac, Hannah Christensen, Nils Weitzel

Abstract:

High-resolution numerical models have been used to develop statistical models of the enhancement of sea surface fluxes resulting from spatial variability of sea-surface wind. In particular, studies have shown that the flux enhancement is not a deterministic function of the resolved state. Previous studies focused on single geographical areas or used a single high-resolution numerical model. This study extends the development of such statistical models by considering six different high-resolution models, four different geographical regions, and three different ten-day periods, allowing for a systematic investigation of the robustness of both the deterministic and stochastic parts of the data-driven parameterization. Results indicate that the deterministic part, based on regressing the unresolved normalized flux onto resolved scale normalized flux and precipitation, is broadly robust across different models, regions, and time periods. The statistical features of the stochastic part of the model (spatial and temporal autocorrelation and parameters of a Gaussian process fit to the regression residual) are also found to be robust and not strongly sensitive to the underlying model, modelled geographical region, or time period studied. Best-fit Gaussian process parameters display robust spatial heterogeneity across models, indicating potential for improvements to the statistical model. These results illustrate the potential for the development of a generic, explicitly stochastic parameterization of sea-surface flux enhancements dependent on wind variability.